Effect Size Consistency Tests (SNP FDR < 0.2, FDR corrected)
XSun
2022-10-15
Last updated: 2022-10-22
Checks: 6 1
Knit directory: factor_analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | ae43c9c | XSun | 2022-10-21 | update |
| html | ae43c9c | XSun | 2022-10-21 | update |
| Rmd | 0706c05 | XSun | 2022-10-17 | update |
| html | 0706c05 | XSun | 2022-10-17 | update |
Introduction
Workflow:
Association test: factor ~ snp + covariates
For the pairs have multiple snps passing FDR < 0.2, do ECT
Results
The number of SNPs passing FDR < 0.2 in association tests
ECT results
Number of pairs passing different ECT FDR cutoff
ECT qqplots and rsq barplots for all pairs have >=3SNPs
ECT qqplots and rsq barplots for all pairs have >=5SNPs
| Version | Author | Date |
|---|---|---|
| ae43c9c | XSun | 2022-10-21 |
| Version | Author | Date |
|---|---|---|
| ae43c9c | XSun | 2022-10-21 |
Top 10 pairs have ECT FDR <0.1
effect size plots for the top 2 pairs
| Version | Author | Date |
|---|---|---|
| ae43c9c | XSun | 2022-10-21 |
| Version | Author | Date |
|---|---|---|
| ae43c9c | XSun | 2022-10-21 |
Detailed results
B cell (CD19+)
Compute ECT FDR only for pairs have >=5 SNPs
Monocyte (CD14+)
Compute ECT FDR only for pairs have >=5 SNPs
Leukocyte (CD15+)
Compute ECT FDR only for pairs have >=5 SNPs
Platelet
Compute ECT FDR only for pairs have >=5 SNPs
T cell (CD4+)
Compute ECT FDR only for pairs have >=5 SNPs
T cell (CD8+)
Compute ECT FDR only for pairs have >=5 SNPs
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] forcats_0.5.1 tidyr_1.2.0 gridExtra_2.3 ggplot2_3.3.5
loaded via a namespace (and not attached):
[1] tidyselect_1.1.2 xfun_0.30 bslib_0.3.1 purrr_0.3.4
[5] lattice_0.20-45 splines_4.2.0 colorspace_2.0-3 vctrs_0.4.1
[9] generics_0.1.2 htmltools_0.5.2 mgcv_1.8-40 yaml_2.3.5
[13] utf8_1.2.2 rlang_1.0.5 jquerylib_0.1.4 later_1.3.0
[17] pillar_1.7.0 glue_1.6.2 withr_2.5.0 DBI_1.1.2
[21] lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0 gtable_0.3.0
[25] workflowr_1.7.0 htmlwidgets_1.5.4 evaluate_0.15 labeling_0.4.2
[29] knitr_1.39 fastmap_1.1.0 crosstalk_1.2.0 httpuv_1.6.5
[33] fansi_1.0.3 highr_0.9 Rcpp_1.0.8.3 DT_0.22
[37] promises_1.2.0.1 scales_1.2.0 jsonlite_1.8.0 farver_2.1.0
[41] fs_1.5.2 digest_0.6.29 stringi_1.7.6 dplyr_1.0.9
[45] grid_4.2.0 rprojroot_2.0.3 cli_3.3.0 tools_4.2.0
[49] magrittr_2.0.3 sass_0.4.1 tibble_3.1.7 crayon_1.5.1
[53] whisker_0.4 pkgconfig_2.0.3 Matrix_1.4-1 ellipsis_0.3.2
[57] assertthat_0.2.1 rmarkdown_2.14 rstudioapi_0.13 R6_2.5.1
[61] nlme_3.1-157 git2r_0.30.1 compiler_4.2.0